Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
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DOI：
10.1093/molbev/msr045
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发表时间：
2011-07-01
影响因子：
10.7
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
--
作者：
dos Reis, Mario;Yang, Ziheng
分子钟提供了一个强有力的方法来估计物种的分歧时间。如果从化石或地质记录中可以获得某些物种分歧时间的信息，它可以用于校准进化树和估计树中所有节点的分歧时间。贝叶斯方法提供了一个自然的框架，将不同来源的信息有关的分歧时间，如化石和分子数据中的信息。目前的序列进化模型是棘手的贝叶斯设置，马尔可夫链蒙特卡罗（MCMC）是用来产生后验分布的发散时间和进化率。这种方法在计算上是昂贵的，因为它涉及似然函数的重复计算。在这里，我们探索使用泰勒展开近似MCMC迭代过程中的可能性。该近似比传统的似然计算快得多。然而，当所提出的参数远离似然峰值时，预计近似是差的。我们探索使用参数变换（平方根，对数和反正弦），以提高近似的似然曲线。我们发现，新的方法，特别是基于反正弦的变换，提供了非常好的近似下放松的时钟模型，也根据全球时钟模型时，全球时钟没有严重违反。当全局时钟严重错误时，该近似值对于全局时钟下的分析而言较差，因此不应使用。结果表明，近似方法可能是有用的贝叶斯断代分析使用大数据集。
The molecular clock provides a powerful way to estimate species divergence times. If information on some species divergence times is available from the fossil or geological record, it can be used to calibrate a phylogeny and estimate divergence times for all nodes in the tree. The Bayesian method provides a natural framework to incorporate different sources of information concerning divergence times, such as information in the fossil and molecular data. Current models of sequence evolution are intractable in a Bayesian setting, and Markov chain Monte Carlo (MCMC) is used to generate the posterior distribution of divergence times and evolutionary rates. This method is computationally expensive, as it involves the repeated calculation of the likelihood function. Here, we explore the use of Taylor expansion to approximate the likelihood during MCMC iteration. The approximation is much faster than conventional likelihood calculation. However, the approximation is expected to be poor when the proposed parameters are far from the likelihood peak. We explore the use of parameter transforms (square root, logarithm, and arcsine) to improve the approximation to the likelihood curve. We found that the new methods, particularly the arcsine-based transform, provided very good approximations under relaxed clock models and also under the global clock model when the global clock is not seriously violated. The approximation is poorer for analysis under the global clock when the global clock is seriously wrong and should thus not be used. The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets.